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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatttgagaatgaaagcgtccaaattgctgctgtaggtttcaagtgtgaattaactgtaaatttccagatgtaatcctttttctgcttgtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATGTTTGATGAAGCAACTCTTGGATGGTTCTCGGATACCCCTAATTACCCGA

Basic information

species Oryza sativa
transcript LOC_Os01g15300.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G146047_T02 (Zea mays), 3'ss of exon 13
aatatttgagaatgaaagcgtccaaattgctgctgtaggtttcaagtgtga-attaactgtaaatttccagatgtaatcctttttctgcttgtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATGTTTGATGAAGCAACTCTTGGATGGTTCTCGGATACCCCTAATTACCCGA
      | ||    | | | || |     |   |  |  ||  | ||  || | |     |   |   ||  ||| |   | |  ||  |||  |    |||| |||||||||||  | ||||||||||| || ||  | ||||| ||| ||| ||||||||||| ||| ||||||||||| |||||| | |   || | |
-----gtaagccccataccctcaaggc--ccatttcaaattcaatgtccgacactcgacattg-tgctcaactgtgaga-tataactttttgcgttc--agGTGGAAAGATTGGCGCGGGAGTGCTTCTTTTTCCTCAGCGAATCGTTTCTGTCTGATGAAGCAAATCTAGGATGGTTCTCAGATACCTCCACGCACACAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86599175|gb|CI355792.1|CI355792
EST:     GATCATGAATAACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTAT
genomic: GATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATT-GGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTAT
EST: gi|88563839|gb|CI494556.1|CI494556
EST:     CGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: CGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|86833164|gb|CI333763.1|CI333763
EST:     ATGAATAACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|88257298|gb|CI359686.1|CI359686
EST:     TTTGCAGGTCATCGTGATCATGAATAACGCAAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: TTTGCAGGTCATCGTGATCATGAATAACGC-AAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|86867385|gb|CI337849.1|CI337849
EST:     ATTTGCAGGTCATCGTGATCATGAATAACGCAAAAGTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|88564021|gb|CI494738.1|CI494738
EST:     ACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|58655440|gb|CK044120.1|CK044120
EST:     ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|88906482|gb|CI375554.1|CI375554
EST:     ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|86599323|gb|CI355940.1|CI355940
EST:     AATAACCCAAAATTTGTTCAGTTACAG                         CTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: AATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|88564544|gb|CI495261.1|CI495261
EST:     CAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: CAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
EST: gi|27548012|gb|CA766115.2|CA766115
EST:     ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAG                         GTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG
genomic: ATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 63 (downstream exon)
Score: 12

GAAGTTTTTCCAGCATATTGCCATCAAGACCTTGTCAGAAAAGATGTCAGATTTGCAGGTCATCGTGATCATGAATAACGCAAAATTTGTTCAGTTACAGgtaaattctc ... gtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATGTTTGATGAAGCAACTCTTGGATGGTTCTCGGATACCCCTAATTACCCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgaattaactgtaaatttccagatgtaatcctttttctgcttgtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATGTTTGATGAAGCAACTCTTGGATGGTTCTCGGATACCCCTAATTACCCGA
     aattaac  putative branch site (score: 12)
                               tcctttttctgcttgt  putative PPT
     aattaactgtaaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatttgagaatgaaagcgtccaaattgctgctgtaggtttcaagtgtgaattaactgtaaatttccagatgtaatcctttttctgcttgtttctctagGTCGAAAGATTGGCAAGAGAGTGCTTCTTATTTCTGGGTGAATCATTTATGTTTGATGAAGCAACTCTTGGATGGTTCTCGGATACCCCTAATTACCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - -gaatgaaa
- - - - - - - - - - - - - -tgctgct